[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run...
[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.
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- modules/Bio/EnsEMBL/BaseAlignFeature.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/BaseAlignFeature.pm
- modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm 4 additions, 5 deletionsmodules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
- modules/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm 4 additions, 0 deletionsmodules/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm
- modules/Bio/EnsEMBL/DBFile/FileAdaptor.pm 1 addition, 2 deletionsmodules/Bio/EnsEMBL/DBFile/FileAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm 15 additions, 12 deletionsmodules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
- modules/Bio/EnsEMBL/External/BlastAdaptor.pm 2 additions, 2 deletionsmodules/Bio/EnsEMBL/External/BlastAdaptor.pm
- modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm 4 additions, 3 deletionsmodules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
- modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm 1 addition, 1 deletion...o/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
- modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
- modules/Bio/EnsEMBL/IndividualSlice.pm 6 additions, 3 deletionsmodules/Bio/EnsEMBL/IndividualSlice.pm
- modules/Bio/EnsEMBL/PaddedSlice.pm 7 additions, 4 deletionsmodules/Bio/EnsEMBL/PaddedSlice.pm
- modules/Bio/EnsEMBL/Pipeline/ChecksumGenerator.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/Pipeline/ChecksumGenerator.pm
- modules/Bio/EnsEMBL/Pipeline/Flatfile/FindDirs.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/Pipeline/Flatfile/FindDirs.pm
- modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm 6 additions, 6 deletionsmodules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm
- modules/Bio/EnsEMBL/ProjectionSegment.pm 3 additions, 0 deletionsmodules/Bio/EnsEMBL/ProjectionSegment.pm
- modules/Bio/EnsEMBL/Registry.pm 6 additions, 6 deletionsmodules/Bio/EnsEMBL/Registry.pm
- modules/Bio/EnsEMBL/StrainSlice.pm 13 additions, 9 deletionsmodules/Bio/EnsEMBL/StrainSlice.pm
- modules/Bio/EnsEMBL/SubSlicedFeature.pm 3 additions, 0 deletionsmodules/Bio/EnsEMBL/SubSlicedFeature.pm
- modules/Bio/EnsEMBL/Utils/Collector.pm 3 additions, 2 deletionsmodules/Bio/EnsEMBL/Utils/Collector.pm
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